salloc -N 1 --exclusive -p amd -t 8:00:00
conda activate star
# working dir
mkdir -p /work/LAS/geetu-lab/arnstrm/hTS_CT27_ST3D_PLAC1_KD
cd /work/LAS/geetu-lab/arnstrm/hTS_CT27_ST3D_PLAC1_KD
mkdir -p 1_data
mkdir -p 2_fastqc
mkdir -p 3_STAR-mapping
mkdir -p 4_featureCounts
mkdir -p 5_multiqc
# file structure
tree -L 1
.
├── 1_data
├── 2_fastqc
├── 3_STAR-mapping
├── 4_featureCounts
└── 5_multiqc

fastaGenome="GRCh38.p13.genome.fa"
gtf="gencode.v42.primary_assembly.annotation.gtf"
STAR --runThreadN $SLURM_JOB_CPUS_PER_NODE \
     --runMode genomeGenerate \
     --genomeDir $(pwd) \
     --genomeFastaFiles $fastaGenome \
     --sjdbGTFfile $gtf \
     --sjdbOverhang 1

#!/bin/bash
conda activate star
index=/work/LAS/geetu-lab/arnstrm/GRCh38_index
read1=$1
read2=$(echo ${read1} | sed 's/_R1_/_R2_/g')
cpus=${SLURM_JOB_CPUS_PER_NODE}
out=$(basename ${read1} | cut -f 1-2 -d "_")
STAR \
--runThreadN ${cpus} \
--genomeDir ${index} \
--outSAMtype BAM SortedByCoordinate \
--quantMode GeneCounts \
--outFilterScoreMinOverLread 0.3 \
--outFilterMatchNminOverLread 0.3 \
--outFileNamePrefix ${out}_ \
--readFilesCommand zcat \
--outWigType bedGraph \
--outWigStrand Unstranded \
--outWigNorm RPM \
--readFilesIn ${read1} ${read2}

for fq in *_R1_*fastq.gz; do
  runSTAR_map.sh $fq;
done

cd 3_STAR-mapping
realpath *.bam > ../4_featureCounts/bam.fofn
cd ../4_featureCounts
gtf="gencode.v42.primary_assembly.annotation.gtf"
while read line; do
ln -s $line;
done
featureCounts \
   -T ${SLURM_CPUS_ON_NODE} \
   -a ${gtf} \
   -t exon \
   -g gene_id \
   -p \
   -B \
   --countReadPairs \
   -o merged_counts.txt \
   --tmpDir ./tmp *.bam

grep -v "^#" merged_counts.txt |\
    cut -f 1,7- |\
    sed 's/_Aligned.sortedByCoord.out.bam//g' > merged_clean-counts.txt
head -n 1 merged_clean-counts.txt > header
grep -Fw -f GRCh38.protein_coding merged_clean-counts.txt > body
cat header body > counts_genes.tsv
rm body head

head -n 1 counts_genes.tsv |\
   tr "\t" "\n" |\
   grep -v "^Geneid" |\
   awk '{print $1"\t"gensub(/..$/, "", 1,$1)}' > info.tsv

save.image(file = "assets/hTS_CT27_ST3D_PLAC1_KD.RData")
save(PLAC1vsSCR.up.pce1, PLAC1vsSCR.dw.pce1, file = "assets/hTS_CT27_ST3D_PLAC1_KD_genelists.RData")

sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] enrichR_3.1                 DT_0.27                    
#>  [3] htmlwidgets_1.5.4           kableExtra_1.3.4           
#>  [5] scales_1.2.1                cowplot_1.1.1              
#>  [7] plotly_4.10.1               TissueEnrich_1.18.0        
#>  [9] GSEABase_1.60.0             graph_1.76.0               
#> [11] annotate_1.76.0             XML_3.99-0.12              
#> [13] AnnotationDbi_1.60.0        ensurer_1.1                
#> [15] biomaRt_2.54.1              reshape2_1.4.4             
#> [17] RColorBrewer_1.1-3          ggrepel_0.9.3              
#> [19] pheatmap_1.0.12             vsn_3.66.0                 
#> [21] DESeq2_1.38.3               SummarizedExperiment_1.28.0
#> [23] Biobase_2.58.0              MatrixGenerics_1.10.0      
#> [25] matrixStats_0.63.0          GenomicRanges_1.50.1       
#> [27] GenomeInfoDb_1.34.3         IRanges_2.32.0             
#> [29] S4Vectors_0.36.0            BiocGenerics_0.44.0        
#> [31] forcats_0.5.2               stringr_1.5.0              
#> [33] dplyr_1.0.10                purrr_1.0.1                
#> [35] readr_2.1.3                 tidyr_1.3.0                
#> [37] tibble_3.1.8                ggplot2_3.4.0              
#> [39] tidyverse_1.3.2            
#> 
#> loaded via a namespace (and not attached):
#>   [1] readxl_1.4.1           backports_1.4.1        BiocFileCache_2.6.1   
#>   [4] systemfonts_1.0.4      plyr_1.8.8             lazyeval_0.2.2        
#>   [7] crosstalk_1.2.0        BiocParallel_1.32.1    digest_0.6.30         
#>  [10] htmltools_0.5.3        fansi_1.0.3            magrittr_2.0.3        
#>  [13] memoise_2.0.1          googlesheets4_1.0.1    tzdb_0.3.0            
#>  [16] limma_3.54.0           Biostrings_2.66.0      modelr_0.1.10         
#>  [19] vroom_1.6.0            svglite_2.1.0          timechange_0.1.1      
#>  [22] rmdformats_1.0.4       prettyunits_1.1.1      colorspace_2.0-3      
#>  [25] blob_1.2.3             rvest_1.0.3            rappdirs_0.3.3        
#>  [28] haven_2.5.1            xfun_0.35              crayon_1.5.2          
#>  [31] RCurl_1.98-1.9         jsonlite_1.8.3         glue_1.6.2            
#>  [34] gtable_0.3.1           gargle_1.2.1           zlibbioc_1.44.0       
#>  [37] XVector_0.38.0         webshot_0.5.4          DelayedArray_0.24.0   
#>  [40] DBI_1.1.3              Rcpp_1.0.9             viridisLite_0.4.1     
#>  [43] xtable_1.8-4           progress_1.2.2         bit_4.0.5             
#>  [46] preprocessCore_1.60.2  httr_1.4.4             ellipsis_0.3.2        
#>  [49] farver_2.1.1           pkgconfig_2.0.3        sass_0.4.3            
#>  [52] dbplyr_2.2.1           locfit_1.5-9.7         utf8_1.2.2            
#>  [55] tidyselect_1.2.0       labeling_0.4.2         rlang_1.1.1           
#>  [58] munsell_0.5.0          cellranger_1.1.0       tools_4.2.2           
#>  [61] cachem_1.0.6           cli_3.4.1              generics_0.1.3        
#>  [64] RSQLite_2.2.18         broom_1.0.1            evaluate_0.18         
#>  [67] fastmap_1.1.0          yaml_2.3.6             knitr_1.41            
#>  [70] bit64_4.0.5            fs_1.5.2               KEGGREST_1.38.0       
#>  [73] xml2_1.3.3             compiler_4.2.2         rstudioapi_0.14       
#>  [76] filelock_1.0.2         curl_4.3.3             png_0.1-7             
#>  [79] affyio_1.68.0          reprex_2.0.2           geneplotter_1.76.0    
#>  [82] bslib_0.4.1            stringi_1.7.8          highr_0.9             
#>  [85] lattice_0.20-45        Matrix_1.5-3           vctrs_0.6.2           
#>  [88] pillar_1.8.1           lifecycle_1.0.3        BiocManager_1.30.19   
#>  [91] jquerylib_0.1.4        data.table_1.14.6      bitops_1.0-7          
#>  [94] R6_2.5.1               affy_1.76.0            bookdown_0.33         
#>  [97] codetools_0.2-18       assertthat_0.2.1       rjson_0.2.21          
#> [100] withr_2.5.0            GenomeInfoDbData_1.2.9 parallel_4.2.2        
#> [103] hms_1.1.2              grid_4.2.2             rmarkdown_2.18        
#> [106] googledrive_2.0.0      lubridate_1.9.0